Drought is a major limiting factor in the cultivation of Sophora alopecuroides in China’s arid and semi-arid regions. This study aimed to identify drought-resistant S. alopecuroides ecotypes and explore key drought tolerance indicators during germination by simulating drought conditions with a 10% PEG-6000 solution, using pure water as a control. Determination of seven germination indicators for S. alopecuroides, including germination rate (GR), germination energy (GE), germination index (GI), vigor index (VI), promptness index (PI), fresh weight (FW), and dry weight (DW), was conducted. Principal component analysis (PCA), membership function, cluster analysis, and linear regression were employed to comprehensively evaluate the drought resistance of thirty-five S. alopecuroides ecotypes. The results showed that drought stress caused reductions in six of the seven indicators across all ecotypes, except for DW, compared to the control. Correlation analysis revealed varying relationships among the indicators, with most showing significant or highly significant correlations. PCA reduced the seven indicators to two independent comprehensive factors, with a cumulative contribution rate of 83.99%. Based on the D-value and cluster analysis, the thirty-five ecotypes were ranked for drought resistance and classified into four categories. The top five drought-tolerant genotypes during the germination stage were identified as Yutian, Alar, Jinghe, Baoding, and Guyuan. Moreover, the stepwise regression model was established and demonstrated that GR, GE, PI, FW, and DW are key indicators for screening and identifying drought-resistant S. alopecuroides ecotypes. This study offers a comprehensive and reliable method for evaluating drought resistance in S. alopecuroides ecotypes and provides a reference for selecting ecotypes for artificial cultivation in Northwestern China.